From 334f158e5a0a04edafa41b5997f7ef46ba9300d6 Mon Sep 17 00:00:00 2001
From: kcibul <kcibul@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 29 Apr 2009 18:05:34 +0000
Subject: [PATCH] added parameters for mapping quality and duplicate filters

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@563 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/HybSelPerformanceWalker.java    | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java
index 5528dd62b..021247832 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java
@@ -2,7 +2,6 @@ package org.broadinstitute.sting.playground.gatk.walkers;
 
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.utils.Pair;
@@ -13,6 +12,9 @@ import java.util.List;
 import net.sf.samtools.SAMRecord;
 
 public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerformanceWalker.TargetInfo> {
+    @Argument(fullName="min_mapq", shortName="mmq", required=false, defaultValue="1", doc="Minimum mapping quality of reads to consider") public Integer MIN_MAPQ;
+    @Argument(fullName="include_duplicates", shortName="idup", required=false, defaultValue="false", doc="consider duplicate reads") public Boolean INCLUDE_DUPLICATE_READS;
+
     public static class TargetInfo {
         public int counts = 0;
 
@@ -35,14 +37,10 @@ public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerforma
         {
             SAMRecord read = reads.get(i);
 
-            // TODO: is there a better way to do this?
-            if (read.getNotPrimaryAlignmentFlag() ||
-                read.getDuplicateReadFlag() ||
-                read.getReadUnmappedFlag() ||
-                read.getMappingQuality() <= -1
-                    ) {
-                continue;
-            }
+            if (read.getNotPrimaryAlignmentFlag()) { continue; }
+            if (read.getReadUnmappedFlag()) { continue; }
+            if (!INCLUDE_DUPLICATE_READS && read.getDuplicateReadFlag()) { continue; }
+            if (read.getMappingQuality() < MIN_MAPQ) { continue; }
             depth++;
         }